Normally, that recommendation is to ensure the user does not attempt to pull full VA out of 1/2 the primary or 1/2 the secondary windings. The core can handle it, but the individual winding likely cannot (or at least will have much poorer regulation than using both). So to be on the safe side, only load each winding to 1/2 of the total VA. You can use both secondary windings individually, but each winding runs at 1/2VA.

No, that's a 100 VA unit, so you can pull 12V-4A out of each winding simultaneously. 12*4=48 VA on each, which is 1/2 the total VA rating of the transformer. The caution is not to try and pull 8A out of one secondary winding, which the copper may not be rated for.

I see in the data sheet they specifically say the copper is oversized, so you probably do have some overload flexibility, but just be aware of the principle.